2.5. TRAJS#
2.5.1. MD Trajectories#
The TRAJS
module performs the extraction of simulated trajectory from GROMACS program. It can be used from the command:
trajs ⟨simbox.gro⟩ [⟨-options⟩]
Note
Simply type trajs
in the terminal and press enter to see the full list of execution options for the module.
2.5.2. Execution Options#
trajs ⟨trajectory.gro/xtc⟩ [⟨-options⟩]
-------------------------------------------------------------------------------------------------
auto : Execute an automated trajectory extraction from simulation files. [-ta](●)(■)
» Description
btrj = 1000 blocks with 10% extraction
» NOTE: this option is recommended in queue systems.
+ #1: Individual Options - (no data analysis) ------------------------------
-itr = I : Extracts position structure #I from the trajectory. [-it](●)(■)⁽†⁾
-ntr = N : Extract N equaly spaced MD steps for truncated trajectory. [-nt](●)(■)
-str = M : Extract equaly spaced frames at every M steps from trajectory. [-st](●)(■)
+ #2: Combinable Options - (with data analysis) ----------------------------
-ctr = [I:J] : Skip I equilibration steps and extract J production steps. [-ct](●)(■)⁽*⁾
-btr = [B:X] : Select frames from B trajectory blocks into X% final steps. [-bt] (■)⁽*⁾
-ptr = [P:D] : Select configurations around pressure P with tolerance ±D (in bar). [-pt] (■)⁽*⁾
+ #3: Output file formats - (GROMACS only) ---------------------------------
-xyz : Output in XYZ file format. [default] [-xy] (■)
-pdb : Output in PDB file format. [-pd] (■)
-gro : Output in GRO file format. [-gr] (■)
+ #4: Other Options --------------------------------------------------------
-prd : Select configuration production steps only and the corresponding properties. [-pr](●)(■)⁽*⁾
-grp : Extract short-ranged non-bonded potential energies. [-gr] (■)⁽*⁾
-nbx : Don´t make corrections for “fragmented” molecules near the box edges. [-nb] (■)
-bak : Save intermediate PDB and XVG files for alternative convertions. [-bk] (■)
-deb : Save intermediate XVG file and create a reconstructed ENT file. [-db] (■)
-for : Force new extraction and override previous PDB file. [-fm](●)(■)
-------------------------------------------------------------------------------------------------
⁽*⁾ Configurable options in automated mode. (●) ORCA available. (■) GROMACS available.
⁽†⁾ Structure position, not configuration step.
2.5.3. Quickstart Examples#
Under construction…